NCM 2023 Houston: Analysis of melanoma evolution using nanopore long-read sequencing data

Beginning in melanin-producing cells (melanocytes), melanoma is the most serious form of skin cancer. While it is highly curable if diagnosed and treated early, most advanced cases can be fatal. Pan-cancer analysis on exome and RNA sequencing data from The Cancer Genome Atlas and other cohorts shows that melanoma is one of the most heterogeneous cancers. A better understanding of the key genomic and epigenomic events that characterize the diverse subclonal populations in melanoma may reveal key insights into what drives its progression and therapeutic resistance. In this study, 24 distinct clonal sublines were derived in vitro from single cells of mouse B2905 melanoma cell line culture, and the genetically homogeneous population from each subline was sequenced using PromethION R10 flowcells. Empowered by the possibility to directly call 5mC base modifications and to perform haplotype phasing with long nanopore sequencing reads, we integrate insights in detected CpG methylation, small variants, and structural variants in our study of melanoma evolution. Preliminary results show that the tumor phylogeny constructed using phased CpG methylation profiles of sublines derived from long-read data corroborates phylogeny based on bulk exome/transcriptome data in a prior work. By associating structural variations and small variants with the constructed phylogeny, our analysis offers a better characterization of the epigenetic mechanism of subclonal evolution in melanoma. In particular, structural variation analysis revealed dozens of clonal and subclonal somatic events, ranging from indels to mosaic chromosomal translocations. These results inform an on-going study on subclone-specific responses to immune checkpoint blockade therapy on a preclinical melanoma model.